Re: [ccp4bb] SEC and MALS

2019-08-27 Thread arjen jakobi 
Dear Natesh,

as Petri pointed out this is a common behavior for proteins/protein
complexes that deviate substantially from a "globular" shape. It is very
typical for elongated proteins/protein complexes containing e.g. extended
coiled-coil regions. These samples will elute much earlier from a SEC
column than expected from their molecular weight, seemingly suggesting
oligomerisation is some form. MALS will allow you to unambigously
characterize their molecular weight independent of their hydrodynamic
radius.

See e.g. https://elifesciences.org/articles/42129 for a recent example. You
will find many if you search for coiled-coil structures or other motifs
that impose elongated shapes.

Best,
Arjen

On Tue, 27 Aug 2019 at 07:57, Natesh Ramanathan 
wrote:

> Dear  Friends,
>
> Can you share your experience with examples of MALS giving lower
> molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg.
> Dimer),  for the same protein sample?
>
>   If you have/know any published paper, can you please point me to
> that reference paper or send me the paper?
>
> Many thanks.
> Best regards,
> Natesh
>
>
> --
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
>
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Assistant Professor,
> School of Biology,
> Indian Institute of Science Education and Research Thiruvananthapuram
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, India
>
> nat...@iisertvm.ac.in
> http://www.researcherid.com/rid/C-4488-2008
> ORCID: http://orcid.org/-0002-1145-5962
> https://publons.com/author/1520837/ramanathan-natesh#profile
> http://faculty.iisertvm.ac.in/natesh
>
> Office Ph. 0091- 471-2778087
>
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>
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Re: [ccp4bb] SEC and MALS

2019-08-27 Thread Rajiv gandhi.s 
Because MALS can capture distinct migrant form of the same protein,
sometimes  protein with disorder and elongated structure behave differently
in  SEC. In SEC we can't distinguish them.  Whereas MALS have scattering at
three different angles,  by that we can captures those multiple forms of
the same protein.
Please provide the image for more information.

On Tue, Aug 27, 2019, 12:30 PM Petri Kursula 
wrote:

> Hi,
> that's typical behaviour for an elongated/disordered molecule, given that
> SEC separates based on hydrodynamic radius, not MW.
> Petri
>
> Petri Kursula
> --
> Professor
> --
> Department of Biomedicine
> University of Bergen, Norway
> http://www.uib.no/en/rg/petrikursula
> 
> petri.kurs...@uib.no 
> --
> Faculty of Biochemistry and Molecular Medicine
> University of Oulu, Finland
> --
>
>
>
>
>
>
> On 27 Aug 2019, at 07:57, Natesh Ramanathan  > wrote:
>
> Dear  Friends,
>
> Can you share your experience with examples of MALS giving lower
> molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg.
> Dimer),  for the same protein sample?
>
>   If you have/know any published paper, can you please point me to
> that reference paper or send me the paper?
>
> Many thanks.
> Best regards,
> Natesh
>
>
> --
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
>
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Assistant Professor,
> School of Biology,
> Indian Institute of Science Education and Research Thiruvananthapuram
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, India
>
> nat...@iisertvm.ac.in
> http://www.researcherid.com/rid/C-4488-2008
> ORCID: http://orcid.org/-0002-1145-5962
> https://publons.com/author/1520837/ramanathan-natesh#profile
> http://faculty.iisertvm.ac.in/natesh
>
> Office Ph. 0091- 471-2778087
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> --
>
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Re: [ccp4bb] SEC and MALS

2019-08-27 Thread Petri Kursula 
Hi,
that's typical behaviour for an elongated/disordered molecule, given that SEC 
separates based on hydrodynamic radius, not MW.
Petri

Petri Kursula
--
Professor 
--
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula 

petri.kurs...@uib.no 
--
Faculty of Biochemistry and Molecular Medicine
University of Oulu, Finland
--






> On 27 Aug 2019, at 07:57, Natesh Ramanathan  wrote:
> 
> Dear  Friends,
> 
> Can you share your experience with examples of MALS giving lower 
> molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg. 
> Dimer),  for the same protein sample?
> 
>   If you have/know any published paper, can you please point me to that 
> reference paper or send me the paper?
> 
> Many thanks.
> Best regards,
> Natesh  
> 
> 
> -- 
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
> 
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Assistant Professor, 
> School of Biology,
> Indian Institute of Science Education and Research Thiruvananthapuram 
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, India
> 
> nat...@iisertvm.ac.in 
> http://www.researcherid.com/rid/C-4488-2008 
> 
> ORCID: http://orcid.org/-0002-1145-5962 
> 
> https://publons.com/author/1520837/ramanathan-natesh#profile 
> 
> http://faculty.iisertvm.ac.in/natesh 
> 
> Office Ph. 0091- 471-2778087
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 



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Re: [ccp4bb] SEC and MALS

2019-08-27 Thread Susan Lea 
What do you mean by mass from SEC? SEC is not a mass determination method

Sent from my iPhone

On 27 Aug 2019, at 06:57, Natesh Ramanathan 
mailto:nat...@iisertvm.ac.in>> wrote:

Dear  Friends,

Can you share your experience with examples of MALS giving lower 
molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg. 
Dimer),  for the same protein sample?

  If you have/know any published paper, can you please point me to that 
reference paper or send me the paper?

Many thanks.
Best regards,
Natesh


--
--
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
--
Dr. Ramanathan Natesh
Assistant Professor,
School of Biology,
Indian Institute of Science Education and Research Thiruvananthapuram 
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

nat...@iisertvm.ac.in
http://www.researcherid.com/rid/C-4488-2008
ORCID: http://orcid.org/-0002-1145-5962
https://publons.com/author/1520837/ramanathan-natesh#profile
http://faculty.iisertvm.ac.in/natesh

Office Ph. 0091- 471-2778087



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Re: [ccp4bb] SEC and MALS

2019-08-27 Thread David Briggs 
Natesh,

Did you use an experimentally determined dn/dc value?

Is it a glycoprotein, or does it have some other modification?

Default dn/dc values are not appropriate for glycoproteins, and will give rise 
to incorrect Mwt values.

Dave

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs


From: CCP4 bulletin board  on behalf of Natesh 
Ramanathan 
Sent: Tuesday, August 27, 2019 6:57:18 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] SEC and MALS

Dear  Friends,

Can you share your experience with examples of MALS giving lower 
molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg. 
Dimer),  for the same protein sample?

  If you have/know any published paper, can you please point me to that 
reference paper or send me the paper?

Many thanks.
Best regards,
Natesh


--
--
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
--
Dr. Ramanathan Natesh
Assistant Professor,
School of Biology,
Indian Institute of Science Education and Research Thiruvananthapuram 
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

nat...@iisertvm.ac.in<mailto:nat...@iisertvm.ac.in>
http://www.researcherid.com/rid/C-4488-2008<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.researcherid.com%2Frid%2FC-4488-2008=02%7C01%7C%7C521f889b923441c7f12408d72ab378ec%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637024822624884263=Rl05IOuaLtwKBGaGqMfp3LbcjHFOMqRRKy2N5P%2Bcxxg%3D=0>
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http://orcid.org/-0002-1145-5962<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Forcid.org%2F-0002-1145-5962=02%7C01%7C%7C521f889b923441c7f12408d72ab378ec%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637024822624884263=7E%2F0fvZAbPxxeeBny97yx8KzzRyVYqMvoZbxeDnhW%2FI%3D=0>
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[ccp4bb] SEC and MALS

2019-08-26 Thread Natesh Ramanathan 
Dear  Friends,

Can you share your experience with examples of MALS giving lower
molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg.
Dimer),  for the same protein sample?

  If you have/know any published paper, can you please point me to that
reference paper or send me the paper?

Many thanks.
Best regards,
Natesh


-- 
--
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
--
Dr. Ramanathan Natesh
Assistant Professor,
School of Biology,
Indian Institute of Science Education and Research Thiruvananthapuram
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

nat...@iisertvm.ac.in
http://www.researcherid.com/rid/C-4488-2008
ORCID: http://orcid.org/-0002-1145-5962
https://publons.com/author/1520837/ramanathan-natesh#profile
http://faculty.iisertvm.ac.in/natesh

Office Ph. 0091- 471-2778087



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